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Protein interface classification by evolutionary analysis

Jose M Duarte, Adam Srebniak, Martin A Schärer, Guido Capitani
2012 BMC Bioinformatics  
In that case, no evolutionary prediction is run and interface classification relies on core size only.  ...  This allows us to formulate an interface assignment even when not enough homologs to the query are available for evolutionary analysis.  ... 
doi:10.1186/1471-2105-13-334 pmid:23259833 pmcid:PMC3556496 fatcat:npelnu2c3vdkpio7u556itfmky

Structure, function, and evolution of transient and obligate protein-protein interactions

J. Mintseris, Z. Weng
2005 Proceedings of the National Academy of Sciences of the United States of America  
from an evolutionary perspective.  ...  We address these and other questions by relying on a carefully curated dataset of protein complex structures.  ...  J.M. is supported by the Department of Energy Computational Science Graduate Fellowship͞ Krell Institute.  ... 
doi:10.1073/pnas.0502667102 pmid:16043700 pmcid:PMC1182425 fatcat:pmdjo4wnancjdcrxiofgzsdsvi

The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures

2019 Nucleic Acids Research  
The Structural Classification of Proteins (SCOP) database is a classification of protein domains organised according to their evolutionary and structural relationships.  ...  We have also improved the database schema, provided a new API and modernised the web interface.  ...  The classification of proteins in SCOP has been constructed mainly manually by visual inspection and analysis.  ... 
doi:10.1093/nar/gkz1064 pmid:31724711 pmcid:PMC7139981 fatcat:i45ut5wpvnafnpu4mmuk4lm25m

Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts

Guido Capitani, Jose M. Duarte, Kumaran Baskaran, Spencer Bliven, Joseph C. Somody
2015 Bioinformatics  
A key issue linked to protein interface classification is the identification of the biological assembly of a crystal structure and the analysis of its symmetry.  ...  This review provides an overview of the concepts and main approaches to protein interface classification: thermodynamic estimation of interface stability, evolutionary approaches based on conservation  ...  Interface classification and docking Protein interface classification has close ties with the field of protein-protein docking.  ... 
doi:10.1093/bioinformatics/btv622 pmid:26508758 pmcid:PMC4743631 fatcat:y5taf2mmlfgtxjjqjb7ghiqvxu

Structural Determinants of Protein Evolution Are Context-Sensitive at the Residue Level

E. A. Franzosa, Y. Xia
2009 Molecular biology and evolution  
The relationship between solvent exposure and evolutionary rate (d N /d S ) is found to be strong, positive, and linear.  ...  burial and a more surprising fixed functional constraint that accompanies any degree of interface involvement.  ...  correct classification rates.  ... 
doi:10.1093/molbev/msp146 pmid:19597162 fatcat:iaqlhlhfafdslib7sq7h6kfxzq

Structural Mapping of Protein Interactions Reveals Differences in Evolutionary Pressures Correlated to mRNA Level and Protein Abundance

Matt Eames, Tanja Kortemme
2007 Structure  
To determine how this constraint affects the evolution of protein interactions, we directly measure evolutionary rates of protein interface, surface, and core residues by structurally mapping domain interactions  ...  Interfaces of proteins with low mRNA levels may have higher evolutionary flexibility and could constitute the raw material for new functions.  ...  Statistical Analysis The R package was used for statistical analysis (Ihaka and Gentleman, 1996) .  ... 
doi:10.1016/j.str.2007.09.010 pmid:17997970 pmcid:PMC2600897 fatcat:tvg2s2ji7nexxev5prmwnt5iwy

ACLAME: A CLAssification of Mobile genetic Elements, update 2010

Raphaël Leplae, Gipsi Lima-Mendez, Ariane Toussaint
2009 Nucleic Acids Research  
The BLAST interface for querying the database has been extended and numerous tools for in-depth analysis of the results have been added.  ...  The ACLAME database is dedicated to the collection, analysis and classification of sequenced mobile genetic elements (MGEs, in particular phages and plasmids).  ...  On the 'Classification' page, users can display the entire graph or only the most closely related MGEs by using the Cytoscape button.  ... 
doi:10.1093/nar/gkp938 pmid:19933762 pmcid:PMC2808911 fatcat:mb35plb5mzfvlh7hxovbd7logy

An analysis of oligomerization interfaces in transmembrane proteins

Jose M Duarte, Nikhil Biyani, Kumaran Baskaran, Guido Capitani
2013 BMC Structural Biology  
In our set, membrane lipids were not found to significantly mediate protein-protein interfaces.  ...  The general features of TM interfaces do not differ much from those of soluble proteins: they are large, tightly packed and possess many interface core residues.  ...  and evolutionary analysis.  ... 
doi:10.1186/1472-6807-13-21 pmid:24134166 pmcid:PMC4015793 fatcat:yijecrbw7rf4honpxpay5tdiey

Understanding protein evolutionary rate by integrating gene co-expression with protein interactions

Kaifang Pang, Chao Cheng, Zhenyu Xuan, Huanye Sheng, Xiaotu Ma
2010 BMC Systems Biology  
Analysis of hub proteins in the Structural Interaction Network further supported ePPID as a better predictor of protein evolutionary rate than the number of distinct binding interfaces and clarified the  ...  slower evolution of co-expressed multi-interface hub proteins over that of other hub proteins.  ...  Acknowledgements XM is supported by NIH grant HG001696 to Michael Q Zhang.  ... 
doi:10.1186/1752-0509-4-179 pmid:21190591 pmcid:PMC3022652 fatcat:yoj6ite67zhvtf4lfigz76yj5a

The Many Faces of Protein–Protein Interactions: A Compendium of Interface Geometry

Wan Kyu Kim, Andreas Henschel, Christof Winter, Michael Schroeder
2006 PLoS Computational Biology  
We show that any evolutionary analysis on interfaces can be skewed by multiple binding orientations and multiple interaction partners.  ...  A systematic classification of protein-protein interfaces is a valuable resource for understanding the principles of molecular recognition and for modelling protein complexes.  ...  Funding through the EFRE (Europä ischer Fonds fü r regionale Entwicklung) projects CODI (Classification of Domain Interfaces), FoldUnfold, GoEverywhere, and the European Union IST projects Sealife and  ... 
doi:10.1371/journal.pcbi.0020124 pmid:17009862 pmcid:PMC1584320 fatcat:npvjydlqa5bcjpfvfmybphjxpq

The Many Faces of Protein-Protein Interactions: A Compendium of Interface Geometry

Wan Kyu Kim, Andreas Henschel, Christof Winter, Michael Schroeder
2005 PLoS Computational Biology  
We show that any evolutionary analysis on interfaces can be skewed by multiple binding orientations and multiple interaction partners.  ...  A systematic classification of protein-protein interfaces is a valuable resource for understanding the principles of molecular recognition and for modelling protein complexes.  ...  Funding through the EFRE (Europä ischer Fonds fü r regionale Entwicklung) projects CODI (Classification of Domain Interfaces), FoldUnfold, GoEverywhere, and the European Union IST projects Sealife and  ... 
doi:10.1371/journal.pcbi.0020124.eor fatcat:cowc33cez5hgvjaxxijkvcatqu

Character and evolution of protein–protein interfaces

Ivica Reš, Olivier Lichtarge
2005 Physical Biology  
Protein-protein interactions create the macromolecular assemblies and sequential signaling pathways essential for cell function.  ...  This paper discusses methods based on multiple sequence alignments of protein homologues and phylogenetic trees.  ...  As a result the analysis of entire interface is always noisy, regardless of how it is defined.  ... 
doi:10.1088/1478-3975/2/2/s04 pmid:16204847 fatcat:bjua3mjjr5gpbgrhzpjlapkoie

Distinguishing crystallographic from biological interfaces in protein complexes: role of intermolecular contacts and energetics for classification

Katarina Elez, Alexandre M J J Bonvin, Anna Vangone
2018 BMC Bioinformatics  
By using a variety of machine learning approaches, we trained a new interface classification predictor based on contacts and interaction energetic features.  ...  We implemented our classification approach into an easy-to-use and fast software, freely available to the scientific community from http://github.com/haddocking/interface-classifier .  ...  Li Xue and Panagiotis Koukos for helpful discussions over data analysis. Further, the authors thank Dr.  ... 
doi:10.1186/s12859-018-2414-9 pmid:30497368 pmcid:PMC6266931 fatcat:77krmd67uzgn3jb2a2qa3kpgri

RIGD: A Database for Intronless Genes in the Rosaceae

Tianzhe Chen, Dandan Meng, Xin Liu, Xi Cheng, Han Wang, Qing Jin, Xiaoyu Xu, Yunpeng Cao, Yongping Cai
2020 Frontiers in Genetics  
In addition, attribute analysis, functional annotations, subcellular localization prediction, and GO analysis are reported. The RIGD allows users to browse, search, and download data with ease.  ...  Most eukaryotic genes are interrupted by one or more introns, and only prokaryotic genomes are composed of mainly single-exon genes without introns.  ...  The funders had no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.  ... 
doi:10.3389/fgene.2020.00868 pmid:32849839 pmcid:PMC7426402 fatcat:uapn3plynrcsbmvpbgtx3er5gm

Prediction of binding hot spot residues by using structural and evolutionary parameters

Roberto Hiroshi Higa, Clésio Luis Tozzi
2009 Genetics and Molecular Biology  
In this work, we present a method for predicting hot spot residues by using a set of structural and evolutionary parameters.  ...  Unlike previous studies, we use a set of parameters which do not depend on the structure of the protein in complex, so that the predictor can also be used when the interface region is unknown.  ...  Structural and evolutionary parameters A set of 43 evolutionary and structural parameters, presented below, were used to characterize an interface residue.  ... 
doi:10.1590/s1415-47572009000300029 pmid:21637529 pmcid:PMC3036045 fatcat:udwbcpemhna5lgriayz2dcoafq
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